From e8327df8595c863d0abdf6a02fdc9ff9dcae6f1f Mon Sep 17 00:00:00 2001
From: Rudraksh Nalbalwar <nalbalwarrudraksh@gmail.com>
Date: Sat, 16 Mar 2024 00:14:14 +0530
Subject: [PATCH 1/3] path replace bug and updated mailmap

---
 .mailmap                           |  2 +
 benchmarks/Untitled.ipynb          | 90 ++++++++++++++++++++++++++++++
 benchmarks/benchmark_run_tardis.py |  6 +-
 tardis/io/atom_data/util.py        | 20 ++++---
 tox.ini                            |  2 +-
 5 files changed, 109 insertions(+), 11 deletions(-)
 create mode 100644 benchmarks/Untitled.ipynb

diff --git a/.mailmap b/.mailmap
index 77a23a6afca..6baefb7b027 100644
--- a/.mailmap
+++ b/.mailmap
@@ -263,3 +263,5 @@ Sarthak Srivastava <sarthaksri592@gmail.com> Sarthak Srivastava <sarthaksri592@g
 
 Kim Lingemann <kim@tg-lingemann.de> kimsina <kim@tg-lingemann.de>
 Kim Lingemann <kim@tg-lingemann.de> kim <kim@tg-lingemann.de>
+
+Rudraksh Nalbalwar <nalbalwarrudraksh@gmail.com> rudrakshnalbalwar <nalbalwarrudraksh@gmail.com>
diff --git a/benchmarks/Untitled.ipynb b/benchmarks/Untitled.ipynb
new file mode 100644
index 00000000000..afac2686aa8
--- /dev/null
+++ b/benchmarks/Untitled.ipynb
@@ -0,0 +1,90 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "666033ca-d3a6-4db5-87f0-f16cc29a7697",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "631fdefc0f0f461389c0bfa714912d9f",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "Iterations:          0/? [00:00<?, ?it/s]"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "6a7ed7ad651f4ceb980a041112e83940",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "Packets:             0/? [00:00<?, ?it/s]"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "from tardis.io.atom_data.util import download_atom_data"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "6d8051cc-3320-47d6-a1a5-89d88f99d94e",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "Atomic Data kurucz_cd23_chianti_H_He already exists in /home/rudraksh-nalbalwar/Downloads/tardis-data/kurucz_cd23_chianti_H_He.h5. Will not download - override with force_download=True.\n"
+     ]
+    }
+   ],
+   "source": [
+    "download_atom_data('kurucz_cd23_chianti_H_He')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "29f0d27a-67bf-48c7-8618-cbee697fe0c9",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.5"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/benchmarks/benchmark_run_tardis.py b/benchmarks/benchmark_run_tardis.py
index 7a62dc5822a..14fd32dc248 100644
--- a/benchmarks/benchmark_run_tardis.py
+++ b/benchmarks/benchmark_run_tardis.py
@@ -3,7 +3,7 @@
 from tardis.io.configuration.config_reader import Configuration
 from tardis import run_tardis
 
-class Benchmarkruntardis:
+class TestBenchmarkruntardis:
     """Class to benchmark the run_tardis function.
     """
     timeout = 200
@@ -13,8 +13,8 @@ def setup(self):
         dir_path = os.path.dirname(os.path.realpath(__file__))
         path = os.path.join(dir_path, "data", filename)
         config = Configuration.from_yaml(path)
-        config.atom_data = "kurucz_cd23_chianti_H_He.h5"
+        config.atom_data = "/home/rudraksh-nalbalwar/Downloads/tardis-data/kurucz_cd23_chianti_H_He.h5"
         self.config = config
     
-    def time_run_tardis(self):
+    def test_run_tardis(self):
         sim = run_tardis(self.config, log_level="ERROR", show_progress_bars=False)
diff --git a/tardis/io/atom_data/util.py b/tardis/io/atom_data/util.py
index 82cff49e183..b967479f6aa 100644
--- a/tardis/io/atom_data/util.py
+++ b/tardis/io/atom_data/util.py
@@ -1,6 +1,8 @@
 import os
 import logging
 
+from pathlib import Path
+
 from tardis.io.configuration.config_internal import get_data_dir
 from tardis.io.atom_data.atom_web_download import (
     get_atomic_repo_config,
@@ -24,18 +26,22 @@ def resolve_atom_data_fname(fname):
         : str
         resolved fpath
     """
+    file_path = Path(fname)
 
-    if os.path.exists(fname):
-        return fname
+    if file_path.exists():
+        return file_path
 
-    fpath = os.path.join(os.path.join(get_data_dir(), fname))
-    if os.path.exists(fpath):
+   # fpath = os.path.join(os.path.join(get_data_dir(), fname))
+    data_dir = Path(get_data_dir())
+    combined_path = data_dir / file_path
+    
+    if combined_path.exists():
         logger.info(
-            f"\n\tAtom Data {fname} not found in local path.\n\tExists in TARDIS Data repo {fpath}"
+            f"\n\tAtom Data {file_path.exist()} not found in local path.\n\tExists in TARDIS Data repo {combined_path}"
         )
-        return fpath
+        return combined_path
 
-    atom_data_name = fname.replace(".h5", "")
+    atom_data_name = file_path.with_suffix("").name
     atom_repo_config = get_atomic_repo_config()
     if atom_data_name in atom_repo_config:
         raise IOError(
diff --git a/tox.ini b/tox.ini
index 477e8824b7c..d380d117025 100644
--- a/tox.ini
+++ b/tox.ini
@@ -18,7 +18,7 @@ indexserver =
 setenv = MPLBACKEND=agg
 
 # Pass through the following environment variables which may be needed for the CI
-passenv = HOME WINDIR LC_ALL LC_CTYPE CC CI TRAVIS
+passenv = HOME,WINDIR,LC_ALL,LC_CTYPE,CC,CI,TRAVIS
 
 # Run the tests in a temporary directory to make sure that we don't import
 # this package from the source tree

From 3068b70972a56f81625693b39fe44e3a1b38cac2 Mon Sep 17 00:00:00 2001
From: Rudraksh Gajanan Nalbalwar
 <126509395+rudrakshnalbalwar@users.noreply.github.com>
Date: Sat, 16 Mar 2024 00:25:58 +0530
Subject: [PATCH 2/3] Delete benchmarks/Untitled.ipynb

---
 benchmarks/Untitled.ipynb | 90 ---------------------------------------
 1 file changed, 90 deletions(-)
 delete mode 100644 benchmarks/Untitled.ipynb

diff --git a/benchmarks/Untitled.ipynb b/benchmarks/Untitled.ipynb
deleted file mode 100644
index afac2686aa8..00000000000
--- a/benchmarks/Untitled.ipynb
+++ /dev/null
@@ -1,90 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "code",
-   "execution_count": 1,
-   "id": "666033ca-d3a6-4db5-87f0-f16cc29a7697",
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "631fdefc0f0f461389c0bfa714912d9f",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "Iterations:          0/? [00:00<?, ?it/s]"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "6a7ed7ad651f4ceb980a041112e83940",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "Packets:             0/? [00:00<?, ?it/s]"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
-   "source": [
-    "from tardis.io.atom_data.util import download_atom_data"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 2,
-   "id": "6d8051cc-3320-47d6-a1a5-89d88f99d94e",
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "Atomic Data kurucz_cd23_chianti_H_He already exists in /home/rudraksh-nalbalwar/Downloads/tardis-data/kurucz_cd23_chianti_H_He.h5. Will not download - override with force_download=True.\n"
-     ]
-    }
-   ],
-   "source": [
-    "download_atom_data('kurucz_cd23_chianti_H_He')"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "29f0d27a-67bf-48c7-8618-cbee697fe0c9",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.11.5"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 5
-}

From 4dd526c18b02c2223a7d65607b3263512bc4a393 Mon Sep 17 00:00:00 2001
From: Rudraksh Gajanan Nalbalwar
 <126509395+rudrakshnalbalwar@users.noreply.github.com>
Date: Sun, 17 Mar 2024 00:59:40 +0530
Subject: [PATCH 3/3] Delete benchmarks/benchmark_run_tardis.py

---
 benchmarks/benchmark_run_tardis.py | 20 --------------------
 1 file changed, 20 deletions(-)
 delete mode 100644 benchmarks/benchmark_run_tardis.py

diff --git a/benchmarks/benchmark_run_tardis.py b/benchmarks/benchmark_run_tardis.py
deleted file mode 100644
index 14fd32dc248..00000000000
--- a/benchmarks/benchmark_run_tardis.py
+++ /dev/null
@@ -1,20 +0,0 @@
-"""Basic TARDIS Benchmark."""
-import os
-from tardis.io.configuration.config_reader import Configuration
-from tardis import run_tardis
-
-class TestBenchmarkruntardis:
-    """Class to benchmark the run_tardis function.
-    """
-    timeout = 200
-    
-    def setup(self):
-        filename = "tardis_configv1_benchmark.yml"
-        dir_path = os.path.dirname(os.path.realpath(__file__))
-        path = os.path.join(dir_path, "data", filename)
-        config = Configuration.from_yaml(path)
-        config.atom_data = "/home/rudraksh-nalbalwar/Downloads/tardis-data/kurucz_cd23_chianti_H_He.h5"
-        self.config = config
-    
-    def test_run_tardis(self):
-        sim = run_tardis(self.config, log_level="ERROR", show_progress_bars=False)